Related papers: Complex DNA Synthesis Sequences
The DNA storage channel is considered, in which the $M$ Deoxyribonucleic acid (DNA) molecules comprising each codeword are stored without order, sampled $N$ times with replacement, and then sequenced over a discrete memoryless channel. For…
We describe properties and constructions of constraint-based codes for DNA-based data storage which account for the maximum repetition length and AT/GC balance. We present algorithms for computing the number of sequences with maximum…
Due to its high data density and longevity, DNA is considered a promising medium for satisfying ever-increasing data storage needs. However, the diversity of errors that occur in DNA sequences makes efficient error-correction a challenging…
We proposed a novel approach to coherent imaging of dynamic samples. The inter-frame similarity of the sample's local structures is found to be a powerful constraint in phasing a sequence of diffraction patterns. We devised a new image…
Deep ensembles have emerged as a powerful technique for improving predictive performance and enhancing model robustness across various applications by leveraging model diversity. However, traditional deep ensemble methods are often…
This paper studies the nucleus decomposition problem, which has been shown to be useful in finding dense substructures in graphs. We present a novel parallel algorithm that is efficient both in theory and in practice. Our algorithm achieves…
The biggest challenge when using DNA as a storage medium is maintaining its stability. The relative occurrence of Guanine (G) and Cytosine (C) is essential for the longevity of DNA. In addition to that, reverse complementary base pairs…
The task of RNA design given a target structure aims to find a sequence that can fold into that structure. It is a computationally hard problem where some version(s) have been proven to be NP-hard. As a result, heuristic methods such as…
Current research on DNA storage usually focuses on the improvement of storage density by developing effective encoding and decoding schemes while lacking the consideration on the uncertainty in ultra-long-term data storage and retention.…
Motivation: Array Comparative Genomic Hybridization (aCGH) is used to scan the entire genome for variations in DNA copy number. A central task in the analysis of aCGH data is the segmentation into groups of probes sharing the same DNA copy…
De novo genome assembly, i.e., rebuilding the sequence of an unknown genome from redundant and erroneous short sequences, is a key but computationally intensive step in many genomics pipelines. The exponential growth of genomic data is…
In this paper, we consider the outer channel for DNA-based data storage. When transmitting over the outer channel, each DNA string is treated as a unit/symbol that would be either correctly received, or erased, or corrupted by uniformly…
Deep Neural Networks (DNNs) suffer from a rapid decrease in performance when trained on a sequence of tasks where only data of the most recent task is available. This phenomenon, known as catastrophic forgetting, prevents DNNs from…
We present a simple route to circumvent kinetic traps which affect many types of DNA nanostructures in their self-assembly process. Using this method, a new 2D DNA lattice made up of short, single-stranded tile (SST) motifs was created.…
Based on the BioBricks standard, restriction synthesis is a novel catabolic iterative DNA synthesis method that utilizes endonucleases to synthesize a query sequence from a reference sequence. In this work, the reference sequence is built…
Deep supervised hashing is essential for efficient storage and search in large-scale image retrieval. Traditional deep supervised hashing models generate single-length hash codes, but this creates a trade-off between efficiency and…
Multisequence Magnetic Resonance Imaging (MRI) provides a more reliable diagnosis in clinical applications through complementary information across sequences. However, in practice, the absence of certain MR sequences is a common problem…
DNA-Encoded Library (DEL) has proven to be a powerful tool that utilizes combinatorially constructed small molecules to facilitate highly-efficient screening assays. These selection experiments, involving multiple stages of washing,…
We propose a new abstraction set (SynopSet) that has a continuum of visual representations for the explanatory analysis of molecular dynamics simulations (MDS) in the DNA nanotechnology domain. By re-purposing the commonly used progress bar…
Simple elastic network models of DNA were developed to reveal the structure-dynamics relationships for several nucleotide sequences. First, we propose a simple all-atom elastic network model of DNA that can explain the profiles of…